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Sample GSM305472 Query DataSets for GSM305472
Status Public on Jul 14, 2009
Title Wild Type Keratinocyte vs CHUK-LoxP Mutant Keratinocyte_rep1
Sample type RNA
 
Channel 1
Source name Wild Type Keratinocyte
Organism Mus musculus
Characteristics Wild type keratinocytes
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from wild type mouse keratinocytes using RNAeasy RNA purification kit (Qiagen, Valencia, CA).
Label Cy3
Label protocol Labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
 
Channel 2
Source name CHUK-LoxP Mutant Keratinocyte
Organism Mus musculus
Characteristics CHUK gene deleted mouse keratinocytes
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from wild type mouse keratinocytes using RNAeasy RNA purification kit (Qiagen, Valencia, CA).
Label Cy5
Label protocol Labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
 
 
Hybridization protocol Manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
Scan protocol Scanning and data acquisitions were performed using Agilent scanner and feature extraction protocol GE2-v5-95 (available at www.agilent.com)
Description The current analysis was carried out to study the changes in the gene expression profiles of CHUK gene deleted mouse keratinocytes compared to wild type mouse keratinocytes
Data processing The data was acquired using Agilent's feature extraction protocol GE2-v5_95 with inbuilt Lowess normalization feature and Log10ratio algorithms, for details visit www.agilent.com
 
Submission date Jul 14, 2008
Last update date Jul 16, 2008
Contact name Yinling Hu
E-mail(s) yhu@mdanderson.org
Phone 512-237 9338
Fax 512-237 2475
Organization name UT M.D.Andreson Cancer Center
Department Carcinogenesis
Lab 3
Street address 1808 Park Road 1C
City Smithville
State/province TX
ZIP/Postal code 78957
Country USA
 
Platform ID GPL4134
Series (1)
GSE12111 IKKα Is Required to Maintain Skin Homeostasis and Prevent Skin Cancer

Data table header descriptions
ID_REF
VALUE Log10 ratio (ie, Log(Redsignal/Greensignal)per feature)
PValueLogRatio Significance level of the Log Ratio computed for feature
gProcessedSignal Cy3 Dye-normalized signal after surrogate algorithm, per channel, used for computation of Log Ratio
rProcessedSignal Cy5 Dye-normalized signal after surrogate algorithm, per channel, used for computation of Log Ratio
gProcessedSigError Cy3 processed signal error
rProcessedSigError Cy5 processed signal error
gMeanSignal Raw mean signal of feature in green (Cy3) channel
rMeanSignal Raw mean signal of feature in red (Cy5) channel
gBGMeanSignal Mean local (local to corresponding feature) back ground signal for Cy3
rBGMeanSignal Mean local (local to corresponding feature) back ground signal for Cy5
gDyeNormSignal Cy3 dye normalized signal
rDyeNormSignal Cy5 dye normalized signal
gDyeNormError The standard error associated with Cy3 dye normalized signal
rDyeNormError The standard error associated with Cy5 dye normalized signal

Data table
ID_REF VALUE PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gMeanSignal rMeanSignal gBGMeanSignal rBGMeanSignal gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError
1 2.22E-01 6.11E-04 4.37E+04 7.28E+04 4.37E+03 7.28E+03 2.36E+04 1.34E+05 3.96E+01 7.01E+01 43672.2 72750.2 4367.23 7275.02
2 0.00E+00 1.00E+00 5.64E+00 3.79E+00 5.64E+00 3.78E+00 6.87E+01 7.64E+01 3.98E+01 7.08E+01 5.63725 3.79177 5.63788 3.77556
3 -3.54E-01 4.90E-01 8.48E+00 3.75E+00 5.72E+00 3.74E+00 7.07E+01 7.91E+01 4.00E+01 7.24E+01 8.47864 3.75454 5.72367 3.73849
4 0.00E+00 1.00E+00 5.63E+00 3.78E+00 5.61E+00 3.77E+00 6.72E+01 7.99E+01 4.00E+01 7.33E+01 5.62665 3.78493 5.61156 3.76876
5 0.00E+00 1.00E+00 5.62E+00 3.78E+00 5.61E+00 3.77E+00 6.69E+01 7.87E+01 4.02E+01 7.21E+01 5.62227 3.78211 5.6051 3.76594
6 0.00E+00 1.00E+00 5.62E+00 3.78E+00 5.61E+00 3.76E+00 6.80E+01 8.55E+01 4.06E+01 7.40E+01 5.61829 3.77959 5.61106 3.76344
7 -2.17E-01 7.19E-01 6.21E+00 3.77E+00 5.64E+00 3.75E+00 6.93E+01 8.52E+01 4.00E+01 7.27E+01 6.20903 3.76912 5.64044 3.75301
8 0.00E+00 1.00E+00 5.61E+00 3.78E+00 5.59E+00 3.76E+00 6.59E+01 8.30E+01 3.96E+01 7.22E+01 5.61229 3.77586 5.59125 3.75972
9 0.00E+00 1.00E+00 5.61E+00 3.77E+00 5.59E+00 3.76E+00 6.57E+01 8.09E+01 4.02E+01 7.36E+01 5.6101 3.77457 5.58894 3.75844
10 0.00E+00 1.00E+00 5.61E+00 3.77E+00 5.59E+00 3.76E+00 6.60E+01 8.32E+01 4.02E+01 7.26E+01 5.60851 3.7737 5.58801 3.75758
11 0.00E+00 1.00E+00 5.61E+00 3.77E+00 5.59E+00 3.76E+00 6.56E+01 8.36E+01 4.00E+01 7.19E+01 5.60747 3.77323 5.58624 3.7571
12 0.00E+00 1.00E+00 5.61E+00 3.77E+00 5.59E+00 3.76E+00 6.43E+01 8.25E+01 4.08E+01 7.22E+01 5.60702 3.77318 5.58571 3.75705
13 1.78E-01 4.99E-02 3.77E+01 5.68E+01 7.06E+00 6.68E+00 8.72E+01 1.85E+02 4.08E+01 7.27E+01 37.7165 56.7724 7.06022 6.67815
14 -1.79E-01 7.77E-01 5.69E+00 3.77E+00 5.62E+00 3.77E+00 6.89E+01 8.99E+01 4.04E+01 7.22E+01 5.69148 3.77308 5.61727 3.76644
15 1.29E-01 1.63E-01 3.81E+01 5.12E+01 7.08E+00 6.21E+00 8.73E+01 1.75E+02 4.04E+01 7.31E+01 38.0845 51.2334 7.08351 6.21441
16 -1.10E-01 1.06E-01 1.25E+02 9.71E+01 1.38E+01 1.03E+01 1.38E+02 2.53E+02 4.07E+01 7.18E+01 125.045 97.1217 13.8248 10.3457
18 0.00E+00 1.00E+00 5.62E+00 3.78E+00 5.59E+00 3.78E+00 6.36E+01 8.99E+01 4.08E+01 7.34E+01 5.61626 3.78165 5.59491 3.77521
19 0.00E+00 1.00E+00 5.62E+00 3.78E+00 5.60E+00 3.77E+00 6.63E+01 8.42E+01 4.02E+01 7.45E+01 5.61974 3.78451 5.60069 3.76834
20 1.53E-01 3.40E-01 1.70E+01 2.42E+01 6.17E+00 4.31E+00 7.52E+01 1.27E+02 4.00E+01 7.39E+01 17.023 24.2057 6.17441 4.30509
21 1.58E-01 2.35E-01 2.14E+01 3.08E+01 6.35E+00 4.69E+00 7.76E+01 1.39E+02 4.00E+01 7.14E+01 21.3793 30.7521 6.35058 4.68919

Total number of rows: 45018

Table truncated, full table size 5612 Kbytes.




Supplementary file Size Download File type/resource
GSM305472.txt.gz 13.0 Mb (ftp)(http) TXT
Processed data included within Sample table
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